Hello,
I guess the problem occurs when you make both cartoon + surface transparent in real-time with transparency_mode=3, the OpenGL renderer in PyMOL simply sucks at compositing multiple transparent objects. try this: set transparency_mode, 1 set backface_cull, 0 set two_sided_lighting, 1 unset ray_shadows then render with ray I hope it helps. Cheers! Kushal Raj Roy Get Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: Khoroshyy Petro <[email protected]> Sent: Friday, February 6, 2026 12:42:10 PM To: pymol-users <[email protected]> Subject: [PyMOL] transparency_mode 3 looks ugly Hi pymollers, I hope this mailing list is still active. I have noticed a decrease in traffic since AI release, but I hope there are still knowledgeable people. I am having trouble with transparency rendering when setting both cartoon and surface to transparent with transparency_mode set to 3. While both surfaces are visible, the resulting image quality is poor. Please see link to the picture for reference. https://photos.app.goo.gl/corhXXpVmdsytmxg6<https://urldefense.com/v3/__https://photos.app.goo.gl/corhXXpVmdsytmxg6__;!!LkSTlj0I!CTMrAviBOj_OX3hjz4gyCljs15ODYJbA8cY62GpxnhBZrHuef3-Z-GYeVvUj-1G6OOWetEFaKSLXxRHxHGiOteg$> Could you provide any guidance on how to resolve this? Best regards, Petro Khoroshyy
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